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protein ligands metals links
Lyase PDB id
2ewe
Jmol
Contents
Protein chain
352 a.a. *
Ligands
ADA-ADA-ADA-ADA
Metals
_CA ×4
Waters ×328
* Residue conservation analysis
PDB id:
2ewe
Name: Lyase
Title: Crystal structure of pectate lyasE C r218k mutant in complex with pentagalacturonic acid
Structure: Pectate lyasE C. Chain: a. Engineered: yes. Mutation: yes
Source: Erwinia chrysanthemi. Organism_taxid: 556. Strain: ec16. Gene: pelc. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.20Å     R-factor:   0.186     R-free:   0.233
Authors: R.D.Scavetta,F.Jurnak
Key ref: R.D.Scavetta et al. (1999). Structure of a plant cell wall fragment complexed to pectate lyase C. Plant Cell, 11, 1081-1092. PubMed id: 10368179 DOI: 10.1105/tpc.11.6.1081
Date:
02-Nov-05     Release date:   15-Nov-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P11073  (PLYC_ERWCH) -  Pectate lyase C
Seq:
Struc: 		375 a.a.
352 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.4.2.2.2  - Pectate lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		Pectin and Pectate Lyases
      Reaction: Eliminative cleavage of pectate to give oligosaccharides with 4-deoxy- alpha-D-gluc-4-enuronosyl groups at their non-reducing ends.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     pathogenesis   1 term 
  Biochemical function     lyase activity     3 terms  

 

 
DOI no: 10.1105/tpc.11.6.1081 Plant Cell 11:1081-1092 (1999)
PubMed id: 10368179  
 
 
Structure of a plant cell wall fragment complexed to pectate lyase C.
R.D.Scavetta, S.R.Herron, A.T.Hotchkiss, N.Kita, N.T.Keen, J.A.Benen, H.C.Kester, J.Visser, F.Jurnak.
 
  ABSTRACT  
 
The three-dimensional structure of a complex between the pectate lyase C (PelC) R218K mutant and a plant cell wall fragment has been determined by x-ray diffraction techniques to a resolution of 2.2 A and refined to a crystallographic R factor of 18.6%. The oligosaccharide substrate, alpha-D-GalpA-([1-->4]-alpha-D-GalpA)3-(1-->4)-D-GalpA , is composed of five galacturonopyranose units (D-GalpA) linked by alpha-(1-->4) glycosidic bonds. PelC is secreted by the plant pathogen Erwinia chrysanthemi and degrades the pectate component of plant cell walls in soft rot diseases. The substrate has been trapped in crystals by using the inactive R218K mutant. Four of the five saccharide units of the substrate are well ordered and represent an atomic view of the pectate component in plant cell walls. The conformation of the pectate fragment is a mix of 21 and 31 right-handed helices. The substrate binds in a cleft, interacting primarily with positively charged groups: either lysine or arginine amino acids on PelC or the four Ca2+ ions found in the complex. The observed protein-oligosaccharide interactions provide a functional explanation for many of the invariant and conserved amino acids in the pectate lyase family of proteins. Because the R218K PelC-galacturonopentaose complex represents an intermediate in the reaction pathway, the structure also reveals important details regarding the enzymatic mechanism. Notably, the results suggest that an arginine, which is invariant in the pectate lyase superfamily, is the amino acid that initiates proton abstraction during the beta elimination cleavage of polygalacturonic acid.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20596756 S.Basu, A.Roy, A.Ghosh, A.Bera, D.Chattopadhyay, and K.Chakrabarti (2011).
Arg²³⁵ is an essential catalytic residue of Bacillus pumilus DKS1 pectate lyase to degum ramie fibre.
  Biodegradation, 22, 153-161.  
20805221 M.L.Garron, and M.Cygler (2010).
Structural and mechanistic classification of uronic acid-containing polysaccharide lyases.
  Glycobiology, 20, 1547-1573.  
18978091 N.Konno, K.Igarashi, N.Habu, M.Samejima, and A.Isogai (2009).
Cloning of the Trichoderma reesei cDNA encoding a glucuronan lyase belonging to a novel polysaccharide lyase family.
  Appl Environ Microbiol, 75, 101-107.  
18535148 D.W.Abbott, and A.B.Boraston (2008).
Structural biology of pectin degradation by Enterobacteriaceae.
  Microbiol Mol Biol Rev, 72, 301.  
  18323615 J.Dabin, M.Jam, M.Czjzek, and G.Michel (2008).
Expression, purification, crystallization and preliminary X-ray analysis of the polysaccharide lyase RB5312 from the marine planctomycete Rhodopirellula baltica.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 224-227.  
18759496 L.J.Pouwels, L.Zhang, N.H.Chan, P.C.Dorrestein, and R.M.Wachter (2008).
Kinetic isotope effect studies on the de novo rate of chromophore formation in fast- and slow-maturing GFP variants.
  Biochemistry, 47, 10111-10122.  
18160124 M.Draye, and P.Van Cutsem (2008).
Pectin methylesterases induce an abrupt increase of acidic pectin during strawberry fruit ripening.
  J Plant Physiol, 165, 1152-1160.  
17459000 A.Collmer, S.Gold, and N.T.Keen (2007).
Noel T. Keen--pioneer leader in molecular plant pathology.
  Annu Rev Phytopathol, 45, 25-42.  
16521140 C.S.Rye, A.Matte, M.Cygler, and S.G.Withers (2006).
An atypical approach identifies TYR234 as the key base catalyst in chondroitin AC lyase.
  Chembiochem, 7, 631-637.  
16834555 R.Sasisekharan, R.Raman, and V.Prabhakar (2006).
Glycomics approach to structure-function relationships of glycosaminoglycans.
  Annu Rev Biomed Eng, 8, 181-231.  
16522010 R.Stern, and M.J.Jedrzejas (2006).
Hyaluronidases: their genomics, structures, and mechanisms of action.
  Chem Rev, 106, 818-839.  
15539389 E.W.Czerwinski, T.Midoro-Horiuti, M.A.White, E.G.Brooks, and R.M.Goldblum (2005).
Crystal structure of Jun a 1, the major cedar pollen allergen from Juniperus ashei, reveals a parallel beta-helical core.
  J Biol Chem, 280, 3740-3746.
PDB code: 1pxz
15717229 M.Soriano, P.Diaz, and F.I.Pastor (2005).
Pectinolytic systems of two aerobic sporogenous bacterial strains with high activity on pectin.
  Curr Microbiol, 50, 114-118.  
15968068 S.A.Douthit, M.Dlakic, D.E.Ohman, and M.J.Franklin (2005).
Epimerase active domain of Pseudomonas aeruginosa AlgG, a protein that contains a right-handed beta-helix.
  J Bacteriol, 187, 4573-4583.  
15159558 H.Novoa De Armas, C.Verboven, C.De Ranter, J.Desair, A.Vande Broek, J.Vanderleyden, and A.Rabijns (2004).
Azospirillum irakense pectate lyase displays a toroidal fold.
  Acta Crystallogr D Biol Crystallogr, 60, 999.
PDB code: 1r76
14997537 J.K.Choi, B.H.Lee, C.H.Chae, and W.Shin (2004).
Computer modeling of the rhamnogalacturonase-"hairy" pectin complex.
  Proteins, 55, 22-33.  
12832805 S.J.Dehdashti, C.N.Doan, K.L.Chao, and M.D.Yoder (2003).
Effect of mutations in the T1.5 loop of pectate lyase A from Erwinia chrysanthemi EC16.
  Acta Crystallogr D Biol Crystallogr, 59, 1339-1342.
PDB codes: 1ooc 1pe9
12162737 D.King, C.Bergmann, R.Orlando, J.A.Benen, H.C.Kester, and J.Visser (2002).
Use of amide exchange mass spectrometry to study conformational changes within the endopolygalacturonase II-homogalacturonan-polygalacturonase inhibiting protein system.
  Biochemistry, 41, 10225-10233.  
12203249 D.King, M.Lumpkin, C.Bergmann, and R.Orlando (2002).
Studying protein-carbohydrate interactions by amide hydrogen/deuterium exchange mass spectrometry.
  Rapid Commun Mass Spectrom, 16, 1569-1574.  
12037303 L.M.Thomas, C.N.Doan, R.L.Oliver, and M.D.Yoder (2002).
Structure of pectate lyase A: comparison to other isoforms.
  Acta Crystallogr D Biol Crystallogr, 58, 1008-1015.
PDB codes: 1jrg 1jta
12221284 S.J.Charnock, I.E.Brown, J.P.Turkenburg, G.W.Black, and G.J.Davies (2002).
Convergent evolution sheds light on the anti-beta -elimination mechanism common to family 1 and 10 polysaccharide lyases.
  Proc Natl Acad Sci U S A, 99, 12067-12072.
PDB codes: 1gxm 1gxn 1gxo
11703654 A.V.Kajava, N.Cheng, R.Cleaver, M.Kessel, M.N.Simon, E.Willery, F.Jacob-Dubuisson, C.Locht, and A.C.Steven (2001).
Beta-helix model for the filamentous haemagglutinin adhesin of Bordetella pertussis and related bacterial secretory proteins.
  Mol Microbiol, 42, 279-292.  
11687632 L.Federici, C.Caprari, B.Mattei, C.Savino, A.Di Matteo, G.De Lorenzo, F.Cervone, and D.Tsernoglou (2001).
Structural requirements of endopolygalacturonase for the interaction with PGIP (polygalacturonase-inhibiting protein).
  Proc Natl Acad Sci U S A, 98, 13425-13430.
PDB code: 1hg8
11717490 M.Akita, A.Suzuki, T.Kobayashi, S.Ito, and T.Yamane (2001).
The first structure of pectate lyase belonging to polysaccharide lyase family 3.
  Acta Crystallogr D Biol Crystallogr, 57, 1786-1792.
PDB code: 1ee6
11468399 S.J.Charnock, I.E.Brown, J.P.Turkenburg, G.W.Black, and G.J.Davies (2001).
Characterization of a novel pectate lyase, Pel10A, from Pseudomonas cellulosa.
  Acta Crystallogr D Biol Crystallogr, 57, 1141-1143.  
11327856 W.Huang, L.Boju, L.Tkalec, H.Su, H.O.Yang, N.S.Gunay, R.J.Linhardt, Y.S.Kim, A.Matte, and M.Cygler (2001).
Active site of chondroitin AC lyase revealed by the structure of enzyme-oligosaccharide complexes and mutagenesis.
  Biochemistry, 40, 2359-2372.
PDB codes: 1hm2 1hm3 1hmu 1hmw
11112543 J.A.Benen, H.C.Kester, L.Parenicová, and J.Visser (2000).
Characterization of Aspergillus niger pectate lyase A.
  Biochemistry, 39, 15563-15569.  
10922032 S.R.Herron, J.A.Benen, R.D.Scavetta, J.Visser, and F.Jurnak (2000).
Structure and function of pectic enzymes: virulence factors of plant pathogens.
  Proc Natl Acad Sci U S A, 97, 8762-8769.  
10759850 Y.Hatada, K.Saito, K.Koike, T.Yoshimatsu, T.Ozawa, T.Kobayashi, and S.Ito (2000).
Deduced amino-acid sequence and possible catalytic residues of a novel pectate lyase from an alkaliphilic strain of Bacillus.
  Eur J Biochem, 267, 2268-2275.  
10567938 J.Colangelo, V.Licon, J.Benen, J.Visser, C.Bergmann, and R.Orlando (1999).
Characterization of the N-linked glycosylation site of recombinant pectate lyase.
  Rapid Commun Mass Spectrom, 13, 2382-2387.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.